In the Mediterranean Sea, organic carbon-rich sapropels have been deposited periodically over the last fifteen million years. Some sapropels are characterized by high contents of the mat-forming, planktonic diatom Pseudosolenia calcar-avis and the planktonic diatom Thalassionema nitzschioides as a result of their mass sinking in autumn (the so-called “fall dump”). The present study shows that fall dump events also occurred in the brackish Baltic Sea around 6300–5800 calibrated years before present (cal yr BP; present = AD 1950). In sediments from the northern Baltic Sea these events are evidenced by high contents of a lipid specific for P. calcar-avis (a C25:2 highly branched isoprenoid alkene) and corroborated by fossil remains of both P. calcar-avis and T. nitzschioides. A biomarker index based on long-chain alkyl diol lipids indicates that mat-forming Proboscia diatoms were also present. High contents of calanoid resting eggs further suggest that the copepod population was stressed being unable to feed on such large diatoms. The fall dump events occurred during a complete stratification of the water column and euxinic conditions, as reflected by the redox-sensitive trace metal uranium, allowing upward diffusion of nutrients and the growth of rhizosolenid mat-forming diatoms in a deep chlorophyll maximum. Synchronous remains of P. calcar-avis in the central Baltic Sea further suggest that these events occurred on a basin-wide scale.